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Table 4 The GATK-LODN method presented good performance in artificial tumor samples. Performance of MuTect and GATK-LODN for artificial tumor samples that had variants with diverse allelic frequencies

From: Optimized pipeline of MuTect and GATK tools to improve the detection of somatic single nucleotide polymorphisms in whole-exome sequencing data

   Artificial Tumor Samples
   Low Frequency Variants (n = 22) VAF: 0.02 – 0.26 Intermediate Frequency Variants (n = 25) VAF: 0.5 – 0.86 High Frequency Variants (n = 25) VAF: 0.97 – 1
MuTect Somatic Candidates 22 25 25
TP 19 25 25
FN 0 0 0
FP 3 0 0
PPV 19/22 25/25 25/25
FDR 3/22 0/25 0/25
GATK-LODN Somatic Candidates 27 32 33
TP 17 23 23
FN 5 5 2
FP 5 7 8
PPV 17/22 23/30 23/31
FDR 5/22 7/30 8/31
  1. TP True positives, FN False negatives, FP False positives, PPV Positive Predictive Value (#TP / #FP + #TP), FDR False Discovery Rate (#FP / #FP + #TP), VAF Variant Allelic Frequency
  2. GATK results were not reported in the table since it detected more than 2200 candidates out of 22 or 25 TPs